rs781292352

Variant names:

• chrX-38805405-G-A
• NM_021242.6:c.459G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-38805405-G-A
• chrX-38805405-G-C
• chrX-38805405-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_021242.6(MID1IP1):​c.459G>A​(p.Gly153Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G153G) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 21)
• Consequence: MID1IP1 NM_021242.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37

Genes affected

MID1IP1 (HGNC:20715): (MID1 interacting protein 1) Predicted to enable identical protein binding activity and protein C-terminus binding activity. Predicted to be involved in several processes, including negative regulation of microtubule depolymerization; positive regulation of fatty acid biosynthetic process; and protein polymerization. Predicted to be located in cytoplasm and microtubule cytoskeleton. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP7: Synonymous conserved (PhyloP=2.37 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MID1IP1	NM_021242.6	c.459G>A	p.Gly153Gly	synonymous_variant	Exon 3 of 3	ENST00000614558.3	NP_067065.1
MID1IP1	NM_001098790.2	c.459G>A	p.Gly153Gly	synonymous_variant	Exon 3 of 3		NP_001092260.1
MID1IP1	NM_001098791.2	c.459G>A	p.Gly153Gly	synonymous_variant	Exon 2 of 2		NP_001092261.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MID1IP1	ENST00000614558.3	c.459G>A	p.Gly153Gly	synonymous_variant	Exon 3 of 3	5	NM_021242.6	ENSP00000483547.1
MID1IP1	ENST00000336949.7	c.459G>A	p.Gly153Gly	synonymous_variant	Exon 2 of 2	1		ENSP00000338706.6
MID1IP1	ENST00000378474.3	c.459G>A	p.Gly153Gly	synonymous_variant	Exon 3 of 3	1		ENSP00000367735.3
MID1IP1	ENST00000457894.5	c.459G>A	p.Gly153Gly	synonymous_variant	Exon 2 of 2	3		ENSP00000416670.1

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.94
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-38664658;